diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c5c12a9..ad312cd 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -8,6 +8,11 @@ This document records all notable changes to This project adheres to `PEP 440 -- Version Identification and Dependency Specification `_. +0.4.4 (22-10-13) +----------------- +- Bug fixes (x- and y-axis vectors failing to generate with imported HDF5 files) +- Minor tweaks and improvements + 0.4.3 (22-08-03) ---------------- - Spectrum and Hsi now moved to **data.spectra**. **This could break your fork if you have custom code.** diff --git a/crikit/CRIkitUI.py b/crikit/CRIkitUI.py index a7755da..0b2a24b 100644 --- a/crikit/CRIkitUI.py +++ b/crikit/CRIkitUI.py @@ -893,9 +893,8 @@ def fileOpenSuccess(self, success): if self.ui.actionUndo_Backup_Enabled.isChecked(): try: _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1]) - except Exception as e: - _traceback.print_exc(limit=1) - print(e) + except Exception: + _traceback.print_exc() print('Error in pickle backup (Undo functionality)') else: self.bcpre.backed_up() diff --git a/crikit/__init__.py b/crikit/__init__.py index 52349c9..0edae99 100644 --- a/crikit/__init__.py +++ b/crikit/__init__.py @@ -14,4 +14,4 @@ * Charles H. Camp Jr. """ -__version__ = '0.4.3' +__version__ = '0.4.4' diff --git a/crikit/io/hdf5.py b/crikit/io/hdf5.py index b88c547..9633125 100644 --- a/crikit/io/hdf5.py +++ b/crikit/io/hdf5.py @@ -21,7 +21,8 @@ __all__ = ['hdf_import_data', 'hdf_import_data_macroraster'] -def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None): +def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None, + interp_kind_spatial='linear', interp_kind_spectral='linear'): """ Import dataset(s) from HDF file with each dset being a single line scan. @@ -107,10 +108,11 @@ def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, c all_xs.extend(curr_x_vec.tolist()) all_ys.extend([curr_y_pos]) - intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind='linear') + intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind=interp_kind_spatial) int_fcn_intensity = interp1d(intfcn(np.arange(curr_slice.shape[0])), - curr_slice, axis=0, bounds_error=False, kind='linear', fill_value='extrapolate') + curr_slice, axis=0, bounds_error=False, kind=interp_kind_spectral, + fill_value='extrapolate') y_idx = find_nearest(y_vec, curr_y_pos)[1] output_cls_instance.data[y_idx, ...] = int_fcn_intensity(x_vec) @@ -169,7 +171,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import) fid[dset_list].read_direct(output_cls_instance.data) - # output_cls_instance.data = fid[dset_list].value output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list) elif isinstance(dset_list, list): if len(dset_list) > 1: @@ -198,9 +199,8 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import) fid[dset_list].read_direct(output_cls_instance.data) else: - output_cls_instance.data = fid[dset_list].value.astype(dset_dtype_import) + output_cls_instance.data = fid[dset_list][:].astype(dset_dtype_import) - # output_cls_instance.data = fid[dset_list].value output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list) elif isinstance(dset_list, list): @@ -222,7 +222,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import) fid[dset_list].read_direct(output_cls_instance.data) - # output_cls_instance.data = fid[dset_list].value output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list) elif isinstance(dset_list, list): if len > 1: @@ -249,7 +248,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None): data = np.zeros(dset_shp, dtype=dset_dtype_import) fid[dset_list].read_direct(data) - # data = fid[dset_list].value meta = lazy5.inspect.get_attrs_dset(fid, dset_list) elif isinstance(dset_list, list): for num, dname in enumerate(dset_list): diff --git a/crikit/io/macros.py b/crikit/io/macros.py index 69e1b77..315df13 100644 --- a/crikit/io/macros.py +++ b/crikit/io/macros.py @@ -15,9 +15,11 @@ __all__ = ['import_hdf_nist_special', 'import_csv_nist_special1'] -def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance): +def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance, + interp_kind_spatial='linear', interp_kind_spectral='linear'): print('\n') - import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance) + import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, + interp_kind_spatial='linear', interp_kind_spectral='linear') if import_success is False: raise ValueError('hdf_import_data_macroraster failed') return False diff --git a/crikit/io/meta_process.py b/crikit/io/meta_process.py index a4db4a0..6c7f29f 100644 --- a/crikit/io/meta_process.py +++ b/crikit/io/meta_process.py @@ -187,8 +187,16 @@ def meta_process(rosetta, output_cls_instance): stop = output_cls_instance.shape[1]-1 units = 'pix' + if isinstance(start, _np.ndarray): + start = start[0] + if isinstance(stop, _np.ndarray): + stop = stop[0] + if isinstance(steps, _np.ndarray): + steps = steps[0] + print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps)) # print('Start: {}, Stop: {}, Steps: {}'.format(start, stop, steps)) + output_cls_instance.x_rep.data = _np.squeeze(_np.linspace(start, stop, steps)) output_cls_instance.x_rep.units = units output_cls_instance.x_rep.label = label @@ -224,6 +232,13 @@ def meta_process(rosetta, output_cls_instance): if isinstance(label, bytes): label = label.decode() + if isinstance(start, _np.ndarray): + start = start[0] + if isinstance(stop, _np.ndarray): + stop = stop[0] + if isinstance(steps, _np.ndarray): + steps = steps[0] + if steps != output_cls_instance.shape[0]: print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps)) print('Warning: {}Steps assigned in meta data ({}) disagrees with datacube size ({})'.format(label, steps, output_cls_instance.shape[0])) diff --git a/docs/build/doctrees/crikit.io.doctree b/docs/build/doctrees/crikit.io.doctree index 34062d0..89fd8a4 100644 Binary files a/docs/build/doctrees/crikit.io.doctree and b/docs/build/doctrees/crikit.io.doctree differ diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo index 4f7216a..f61d787 100644 --- a/docs/build/html/.buildinfo +++ b/docs/build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 79acee3da732a2077d4e910c14203444 +config: 126e78dc37b63522d8e4d07dce0d2051 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/_modules/crikit/CRIkitUI.html b/docs/build/html/_modules/crikit/CRIkitUI.html index 8b9477e..5bf8d95 100644 --- a/docs/build/html/_modules/crikit/CRIkitUI.html +++ b/docs/build/html/_modules/crikit/CRIkitUI.html @@ -5,7 +5,7 @@ - crikit.CRIkitUI — CRIKit2 0.4.3 documentation + crikit.CRIkitUI — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

Navigation

  • modules |
  • - + @@ -931,9 +931,8 @@

    Source code for crikit.CRIkitUI

             if self.ui.actionUndo_Backup_Enabled.isChecked():
                 try:
                     _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
    -            except Exception as e:
    -                _traceback.print_exc(limit=1)
    -                print(e)
    +            except Exception:
    +                _traceback.print_exc()
                     print('Error in pickle backup (Undo functionality)')
                 else:
                     self.bcpre.backed_up()
    @@ -3908,7 +3907,7 @@ 

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/algorithms/kk.html b/docs/build/html/_modules/crikit/cri/algorithms/kk.html index eed0de9..b42b65b 100644 --- a/docs/build/html/_modules/crikit/cri/algorithms/kk.html +++ b/docs/build/html/_modules/crikit/cri/algorithms/kk.html @@ -5,7 +5,7 @@ - crikit.cri.algorithms.kk — CRIKit2 0.4.3 documentation + crikit.cri.algorithms.kk — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -274,7 +274,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/error_correction.html b/docs/build/html/_modules/crikit/cri/error_correction.html index edbe546..9b383c4 100644 --- a/docs/build/html/_modules/crikit/cri/error_correction.html +++ b/docs/build/html/_modules/crikit/cri/error_correction.html @@ -5,7 +5,7 @@ - crikit.cri.error_correction — CRIKit2 0.4.3 documentation + crikit.cri.error_correction — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -355,7 +355,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/kk.html b/docs/build/html/_modules/crikit/cri/kk.html index d354005..deae306 100644 --- a/docs/build/html/_modules/crikit/cri/kk.html +++ b/docs/build/html/_modules/crikit/cri/kk.html @@ -5,7 +5,7 @@ - crikit.cri.kk — CRIKit2 0.4.3 documentation + crikit.cri.kk — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -363,7 +363,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/merge_nrbs.html b/docs/build/html/_modules/crikit/cri/merge_nrbs.html index 30323fd..e0f4024 100644 --- a/docs/build/html/_modules/crikit/cri/merge_nrbs.html +++ b/docs/build/html/_modules/crikit/cri/merge_nrbs.html @@ -5,7 +5,7 @@ - crikit.cri.merge_nrbs — CRIKit2 0.4.3 documentation + crikit.cri.merge_nrbs — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -175,7 +175,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html b/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html index 2d03c9b..71570f6 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_hilbert.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_hilbert — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_hilbert — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -116,7 +116,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_kk.html b/docs/build/html/_modules/crikit/cri/tests/test_kk.html index f89b2dc..d005ec9 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_kk.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_kk.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_kk — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_kk — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -159,7 +159,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html b/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html index aa7e76e..62f56f6 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_kk_alg.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_kk_alg — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_kk_alg — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -112,7 +112,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_merge_nrbs.html b/docs/build/html/_modules/crikit/cri/tests/test_merge_nrbs.html index aed1f6c..65b6a6b 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_merge_nrbs.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_merge_nrbs.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_merge_nrbs — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_merge_nrbs — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -93,7 +93,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_pec.html b/docs/build/html/_modules/crikit/cri/tests/test_pec.html index 93f9a91..e54e9b2 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_pec.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_pec.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_pec — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_pec — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -442,7 +442,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/cri/tests/test_sec.html b/docs/build/html/_modules/crikit/cri/tests/test_sec.html index 9d16642..f874932 100644 --- a/docs/build/html/_modules/crikit/cri/tests/test_sec.html +++ b/docs/build/html/_modules/crikit/cri/tests/test_sec.html @@ -5,7 +5,7 @@ - crikit.cri.tests.test_sec — CRIKit2 0.4.3 documentation + crikit.cri.tests.test_sec — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -112,7 +112,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/factorized.html b/docs/build/html/_modules/crikit/data/factorized.html index 33808a8..3fece9e 100644 --- a/docs/build/html/_modules/crikit/data/factorized.html +++ b/docs/build/html/_modules/crikit/data/factorized.html @@ -5,7 +5,7 @@ - crikit.data.factorized — CRIKit2 0.4.3 documentation + crikit.data.factorized — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -127,7 +127,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/frequency.html b/docs/build/html/_modules/crikit/data/frequency.html index ffbbbd8..65226a4 100644 --- a/docs/build/html/_modules/crikit/data/frequency.html +++ b/docs/build/html/_modules/crikit/data/frequency.html @@ -5,7 +5,7 @@ - crikit.data.frequency — CRIKit2 0.4.3 documentation + crikit.data.frequency — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -534,7 +534,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/mosaic.html b/docs/build/html/_modules/crikit/data/mosaic.html index 3de90cd..df3bb00 100644 --- a/docs/build/html/_modules/crikit/data/mosaic.html +++ b/docs/build/html/_modules/crikit/data/mosaic.html @@ -5,7 +5,7 @@ - crikit.data.mosaic — CRIKit2 0.4.3 documentation + crikit.data.mosaic — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -443,7 +443,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/replicate.html b/docs/build/html/_modules/crikit/data/replicate.html index ad5a9bb..b375f13 100644 --- a/docs/build/html/_modules/crikit/data/replicate.html +++ b/docs/build/html/_modules/crikit/data/replicate.html @@ -5,7 +5,7 @@ - crikit.data.replicate — CRIKit2 0.4.3 documentation + crikit.data.replicate — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -250,7 +250,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/spectra.html b/docs/build/html/_modules/crikit/data/spectra.html index 9da3a52..fb41101 100644 --- a/docs/build/html/_modules/crikit/data/spectra.html +++ b/docs/build/html/_modules/crikit/data/spectra.html @@ -5,7 +5,7 @@ - crikit.data.spectra — CRIKit2 0.4.3 documentation + crikit.data.spectra — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -982,7 +982,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/tests/test_hsi.html b/docs/build/html/_modules/crikit/data/tests/test_hsi.html index f595941..57f1769 100644 --- a/docs/build/html/_modules/crikit/data/tests/test_hsi.html +++ b/docs/build/html/_modules/crikit/data/tests/test_hsi.html @@ -5,7 +5,7 @@ - crikit.data.tests.test_hsi — CRIKit2 0.4.3 documentation + crikit.data.tests.test_hsi — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -188,7 +188,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/tests/test_mosaic.html b/docs/build/html/_modules/crikit/data/tests/test_mosaic.html index d7d21a6..ae41592 100644 --- a/docs/build/html/_modules/crikit/data/tests/test_mosaic.html +++ b/docs/build/html/_modules/crikit/data/tests/test_mosaic.html @@ -5,7 +5,7 @@ - crikit.data.tests.test_mosaic — CRIKit2 0.4.3 documentation + crikit.data.tests.test_mosaic — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -536,7 +536,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/tests/test_mosaic_hdf.html b/docs/build/html/_modules/crikit/data/tests/test_mosaic_hdf.html index 6bcf042..2cd37ee 100644 --- a/docs/build/html/_modules/crikit/data/tests/test_mosaic_hdf.html +++ b/docs/build/html/_modules/crikit/data/tests/test_mosaic_hdf.html @@ -5,7 +5,7 @@ - crikit.data.tests.test_mosaic_hdf — CRIKit2 0.4.3 documentation + crikit.data.tests.test_mosaic_hdf — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -321,7 +321,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/tests/test_spectra.html b/docs/build/html/_modules/crikit/data/tests/test_spectra.html index 18f0078..5978b30 100644 --- a/docs/build/html/_modules/crikit/data/tests/test_spectra.html +++ b/docs/build/html/_modules/crikit/data/tests/test_spectra.html @@ -5,7 +5,7 @@ - crikit.data.tests.test_spectra — CRIKit2 0.4.3 documentation + crikit.data.tests.test_spectra — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -188,7 +188,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/data/tests/test_spectrum.html b/docs/build/html/_modules/crikit/data/tests/test_spectrum.html index 6be11cd..89810ad 100644 --- a/docs/build/html/_modules/crikit/data/tests/test_spectrum.html +++ b/docs/build/html/_modules/crikit/data/tests/test_spectrum.html @@ -5,7 +5,7 @@ - crikit.data.tests.test_spectrum — CRIKit2 0.4.3 documentation + crikit.data.tests.test_spectrum — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -182,7 +182,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/datasets/model.html b/docs/build/html/_modules/crikit/datasets/model.html index ba4a8dd..5270708 100644 --- a/docs/build/html/_modules/crikit/datasets/model.html +++ b/docs/build/html/_modules/crikit/datasets/model.html @@ -5,7 +5,7 @@ - crikit.datasets.model — CRIKit2 0.4.3 documentation + crikit.datasets.model — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -219,7 +219,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/io/csv_nist.html b/docs/build/html/_modules/crikit/io/csv_nist.html index 023aa2c..cbdb50e 100644 --- a/docs/build/html/_modules/crikit/io/csv_nist.html +++ b/docs/build/html/_modules/crikit/io/csv_nist.html @@ -5,7 +5,7 @@ - crikit.io.csv_nist — CRIKit2 0.4.3 documentation + crikit.io.csv_nist — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -322,7 +322,7 @@

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/io/hdf5.html b/docs/build/html/_modules/crikit/io/hdf5.html index 4e009fb..ab33204 100644 --- a/docs/build/html/_modules/crikit/io/hdf5.html +++ b/docs/build/html/_modules/crikit/io/hdf5.html @@ -5,7 +5,7 @@ - crikit.io.hdf5 — CRIKit2 0.4.3 documentation + crikit.io.hdf5 — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -59,7 +59,8 @@

    Source code for crikit.io.hdf5

     __all__ = ['hdf_import_data', 'hdf_import_data_macroraster']
     
     
    -
    [docs]def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None): +
    [docs]def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None, + interp_kind_spatial='linear', interp_kind_spectral='linear'): """ Import dataset(s) from HDF file with each dset being a single line scan. @@ -145,10 +146,11 @@

    Source code for crikit.io.hdf5

                 all_xs.extend(curr_x_vec.tolist())
                 all_ys.extend([curr_y_pos])
     
    -            intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind='linear')
    +            intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind=interp_kind_spatial)
     
                 int_fcn_intensity = interp1d(intfcn(np.arange(curr_slice.shape[0])),
    -                                         curr_slice, axis=0, bounds_error=False, kind='linear', fill_value='extrapolate')
    +                                         curr_slice, axis=0, bounds_error=False, kind=interp_kind_spectral,
    +                                         fill_value='extrapolate')
     
                 y_idx = find_nearest(y_vec, curr_y_pos)[1]
                 output_cls_instance.data[y_idx, ...] = int_fcn_intensity(x_vec)
    @@ -207,7 +209,6 @@ 

    Source code for crikit.io.hdf5

                     output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                     fid[dset_list].read_direct(output_cls_instance.data)
     
    -                # output_cls_instance.data = fid[dset_list].value
                     output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
                 elif isinstance(dset_list, list):
                     if len(dset_list) > 1:
    @@ -236,9 +237,8 @@ 

    Source code for crikit.io.hdf5

                         output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                         fid[dset_list].read_direct(output_cls_instance.data)
                     else:
    -                    output_cls_instance.data = fid[dset_list].value.astype(dset_dtype_import)
    +                    output_cls_instance.data = fid[dset_list][:].astype(dset_dtype_import)
     
    -                # output_cls_instance.data = fid[dset_list].value
                     output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
     
                 elif isinstance(dset_list, list):
    @@ -260,7 +260,6 @@ 

    Source code for crikit.io.hdf5

                     output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                     fid[dset_list].read_direct(output_cls_instance.data)
     
    -                # output_cls_instance.data = fid[dset_list].value
                     output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
                 elif isinstance(dset_list, list):
                     if len > 1:
    @@ -287,7 +286,6 @@ 

    Source code for crikit.io.hdf5

                     data = np.zeros(dset_shp, dtype=dset_dtype_import)
                     fid[dset_list].read_direct(data)
     
    -                # data = fid[dset_list].value
                     meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
                 elif isinstance(dset_list, list):
                     for num, dname in enumerate(dset_list):
    @@ -404,7 +402,7 @@ 

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/alter.html b/docs/build/html/_modules/crikit/io/lazy5/alter.html index 5ef87de..60385e0 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/alter.html +++ b/docs/build/html/_modules/crikit/io/lazy5/alter.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.alter — CRIKit2 0.4.3 documentation + crikit.io.lazy5.alter — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

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  • - + @@ -226,7 +226,7 @@

    Navigation

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/config.html b/docs/build/html/_modules/crikit/io/lazy5/config.html index a03a3d5..5fb4941 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/config.html +++ b/docs/build/html/_modules/crikit/io/lazy5/config.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.config — CRIKit2 0.4.3 documentation + crikit.io.lazy5.config — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -72,7 +72,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/create.html b/docs/build/html/_modules/crikit/io/lazy5/create.html index 82b351a..35504db 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/create.html +++ b/docs/build/html/_modules/crikit/io/lazy5/create.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.create — CRIKit2 0.4.3 documentation + crikit.io.lazy5.create — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -148,7 +148,7 @@

    Navigation

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/inspect.html b/docs/build/html/_modules/crikit/io/lazy5/inspect.html index ce08c6e..86bb6f3 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/inspect.html +++ b/docs/build/html/_modules/crikit/io/lazy5/inspect.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.inspect — CRIKit2 0.4.3 documentation + crikit.io.lazy5.inspect — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -355,7 +355,7 @@

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    Navigation

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  • - + @@ -164,7 +164,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/tests/test_alter.html b/docs/build/html/_modules/crikit/io/lazy5/tests/test_alter.html index 41ebe95..9ffeeda 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/tests/test_alter.html +++ b/docs/build/html/_modules/crikit/io/lazy5/tests/test_alter.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.tests.test_alter — CRIKit2 0.4.3 documentation + crikit.io.lazy5.tests.test_alter — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

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  • - + @@ -414,7 +414,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/tests/test_create.html b/docs/build/html/_modules/crikit/io/lazy5/tests/test_create.html index 3d5d35d..2f34db1 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/tests/test_create.html +++ b/docs/build/html/_modules/crikit/io/lazy5/tests/test_create.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.tests.test_create — CRIKit2 0.4.3 documentation + crikit.io.lazy5.tests.test_create — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

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  • - + @@ -170,7 +170,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/tests/test_inspect.html b/docs/build/html/_modules/crikit/io/lazy5/tests/test_inspect.html index 92383e8..7768e6b 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/tests/test_inspect.html +++ b/docs/build/html/_modules/crikit/io/lazy5/tests/test_inspect.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.tests.test_inspect — CRIKit2 0.4.3 documentation + crikit.io.lazy5.tests.test_inspect — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -415,7 +415,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/tests/test_nonh5utils.html b/docs/build/html/_modules/crikit/io/lazy5/tests/test_nonh5utils.html index 878f8e2..b7fe9e5 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/tests/test_nonh5utils.html +++ b/docs/build/html/_modules/crikit/io/lazy5/tests/test_nonh5utils.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.tests.test_nonh5utils — CRIKit2 0.4.3 documentation + crikit.io.lazy5.tests.test_nonh5utils — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -197,7 +197,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/tests/test_ui.html b/docs/build/html/_modules/crikit/io/lazy5/tests/test_ui.html index 97d19e0..a8ba8f4 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/tests/test_ui.html +++ b/docs/build/html/_modules/crikit/io/lazy5/tests/test_ui.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.tests.test_ui — CRIKit2 0.4.3 documentation + crikit.io.lazy5.tests.test_ui — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -230,7 +230,7 @@

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  • - + @@ -309,7 +309,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/lazy5/ui/qt_HdfLoad.html b/docs/build/html/_modules/crikit/io/lazy5/ui/qt_HdfLoad.html index 6cd15f8..940b1ef 100644 --- a/docs/build/html/_modules/crikit/io/lazy5/ui/qt_HdfLoad.html +++ b/docs/build/html/_modules/crikit/io/lazy5/ui/qt_HdfLoad.html @@ -5,7 +5,7 @@ - crikit.io.lazy5.ui.qt_HdfLoad — CRIKit2 0.4.3 documentation + crikit.io.lazy5.ui.qt_HdfLoad — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -224,7 +224,7 @@

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  • - + @@ -160,7 +160,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/io/macros.html b/docs/build/html/_modules/crikit/io/macros.html index 22969c7..3b1f62b 100644 --- a/docs/build/html/_modules/crikit/io/macros.html +++ b/docs/build/html/_modules/crikit/io/macros.html @@ -5,7 +5,7 @@ - crikit.io.macros — CRIKit2 0.4.3 documentation + crikit.io.macros — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -53,9 +53,11 @@

    Source code for crikit.io.macros

     __all__ = ['import_hdf_nist_special', 'import_csv_nist_special1']
     
     
    -def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance):
    +def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance, 
    +                                 interp_kind_spatial='linear', interp_kind_spectral='linear'):
         print('\n')
    -    import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance)
    +    import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance,
    +                                                  interp_kind_spatial='linear', interp_kind_spectral='linear')
         if import_success is False:
             raise ValueError('hdf_import_data_macroraster failed')
             return False
    @@ -182,7 +184,7 @@ 

    Navigation

  • modules |
  • - + diff --git a/docs/build/html/_modules/crikit/io/meta_configs.html b/docs/build/html/_modules/crikit/io/meta_configs.html index 9313028..04bc71d 100644 --- a/docs/build/html/_modules/crikit/io/meta_configs.html +++ b/docs/build/html/_modules/crikit/io/meta_configs.html @@ -5,7 +5,7 @@ - crikit.io.meta_configs — CRIKit2 0.4.3 documentation + crikit.io.meta_configs — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -171,7 +171,7 @@

    Navigation

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  • - + diff --git a/docs/build/html/_modules/crikit/io/meta_process.html b/docs/build/html/_modules/crikit/io/meta_process.html index f34604a..ab8d552 100644 --- a/docs/build/html/_modules/crikit/io/meta_process.html +++ b/docs/build/html/_modules/crikit/io/meta_process.html @@ -5,7 +5,7 @@ - crikit.io.meta_process — CRIKit2 0.4.3 documentation + crikit.io.meta_process — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
  • - + @@ -225,8 +225,16 @@

    Source code for crikit.io.meta_process

                     stop = output_cls_instance.shape[1]-1
                     units = 'pix'
     
    +            if isinstance(start, _np.ndarray):
    +                start = start[0]
    +            if isinstance(stop, _np.ndarray):
    +                stop = stop[0]
    +            if isinstance(steps, _np.ndarray):
    +                steps = steps[0]
    +
                 print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
                 # print('Start: {}, Stop: {}, Steps: {}'.format(start, stop, steps))
    +
                 output_cls_instance.x_rep.data = _np.squeeze(_np.linspace(start, stop, steps))
                 output_cls_instance.x_rep.units = units
                 output_cls_instance.x_rep.label = label
    @@ -262,6 +270,13 @@ 

    Source code for crikit.io.meta_process

                 if isinstance(label, bytes):
                     label = label.decode()
     
    +            if isinstance(start, _np.ndarray):
    +                start = start[0]
    +            if isinstance(stop, _np.ndarray):
    +                stop = stop[0]
    +            if isinstance(steps, _np.ndarray):
    +                steps = steps[0]
    +                
                 if steps != output_cls_instance.shape[0]:
                     print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
                     print('Warning: {}Steps assigned in meta data ({}) disagrees with datacube size ({})'.format(label, steps, output_cls_instance.shape[0]))
    @@ -354,7 +369,7 @@ 

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  • - + diff --git a/docs/build/html/_modules/crikit/io/tests/test_hdf5.html b/docs/build/html/_modules/crikit/io/tests/test_hdf5.html index 3229cf2..bf53f16 100644 --- a/docs/build/html/_modules/crikit/io/tests/test_hdf5.html +++ b/docs/build/html/_modules/crikit/io/tests/test_hdf5.html @@ -5,7 +5,7 @@ - crikit.io.tests.test_hdf5 — CRIKit2 0.4.3 documentation + crikit.io.tests.test_hdf5 — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -255,7 +255,7 @@

    Navigation

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  • - + @@ -723,7 +723,7 @@

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  • - + @@ -335,7 +335,7 @@

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  • - + @@ -328,7 +328,7 @@

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  • - + @@ -328,7 +328,7 @@

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  • - + @@ -118,7 +118,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html b/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html index 02b9818..7ca6f1c 100644 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html +++ b/docs/build/html/_modules/crikit/preprocess/algorithms/abstract_als.html @@ -5,7 +5,7 @@ - crikit.preprocess.algorithms.abstract_als — CRIKit2 0.4.3 documentation + crikit.preprocess.algorithms.abstract_als — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -170,7 +170,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/als.html b/docs/build/html/_modules/crikit/preprocess/algorithms/als.html index f18fbfe..57ccae1 100644 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/als.html +++ b/docs/build/html/_modules/crikit/preprocess/algorithms/als.html @@ -5,7 +5,7 @@ - crikit.preprocess.algorithms.als — CRIKit2 0.4.3 documentation + crikit.preprocess.algorithms.als — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -290,7 +290,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/anscombe.html b/docs/build/html/_modules/crikit/preprocess/algorithms/anscombe.html index 9d240fa..5a9c0ef 100644 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/anscombe.html +++ b/docs/build/html/_modules/crikit/preprocess/algorithms/anscombe.html @@ -5,7 +5,7 @@ - crikit.preprocess.algorithms.anscombe — CRIKit2 0.4.3 documentation + crikit.preprocess.algorithms.anscombe — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -484,7 +484,7 @@

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  • - + diff --git a/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html b/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html index 61ed98d..ce58433 100644 --- a/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html +++ b/docs/build/html/_modules/crikit/preprocess/algorithms/arpls.html @@ -5,7 +5,7 @@ - crikit.preprocess.algorithms.arpls — CRIKit2 0.4.3 documentation + crikit.preprocess.algorithms.arpls — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

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  • - + @@ -244,7 +244,7 @@

    Navigation

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  • - + diff --git a/docs/build/html/_modules/crikit/preprocess/crop.html b/docs/build/html/_modules/crikit/preprocess/crop.html index 39e4e0c..ad1dfe7 100644 --- a/docs/build/html/_modules/crikit/preprocess/crop.html +++ b/docs/build/html/_modules/crikit/preprocess/crop.html @@ -5,7 +5,7 @@ - crikit.preprocess.crop — CRIKit2 0.4.3 documentation + crikit.preprocess.crop — CRIKit2 0.4.4 documentation @@ -24,7 +24,7 @@

    Navigation

  • modules |
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  • modules |
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    Navigation

  • modules |
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  • modules |
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    Navigation

  • modules |
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  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

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    Navigation

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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

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    Navigation

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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

  • modules |
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    Navigation

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    Navigation

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    Navigation

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    Navigation

  • modules |
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    Navigation

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    Navigation

  • modules |
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    Navigation

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    Navigation

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    Navigation

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    Navigation

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    Navigation

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  • modules |
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    Navigation

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  • modules |
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  • modules |
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